Name | Description | Type | Package | Framework |
AbstractAsyncWriter | Abstract class that is designed to be extended and specialized to provide an asynchronous wrapper around any kind of Writer class that takes an object and writes it out somehow. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractBAMFileIndex | Provides basic, generic capabilities to be used reading BAM index files. | Class | htsjdk.samtools | HtsJDK |
|
AbstractBitCodec | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
AbstractFeatureCodec | Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implement FeatureCodec. | Class | htsjdk.tribble | HtsJDK |
|
AbstractFeatureReader | the feature reader class, which uses indices and codecs to read in Tribble file formats. | Class | htsjdk.tribble | HtsJDK |
|
AbstractIndex | An abstract implementation of the index class. | Class | htsjdk.tribble.index | HtsJDK |
|
AbstractIterator | Base class of implementing iterators. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractJavascriptFilter | Javascript filter with HEADER type containing TYPE records. | Class | htsjdk.samtools.filter | HtsJDK |
|
AbstractProgressLogger | Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractReader | | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
AbstractSAMHeaderRecord | Base class for the various concrete records in a SAM header, providing uniform access to the attributes. | Class | htsjdk.samtools | HtsJDK |
|
AbstractVCFCodec | | Class | htsjdk.variant.vcf | HtsJDK |
|
AggregateFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
AlignedFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
AlignmentBlock | Represents the contiguous alignment of a subset of read bases to a reference sequence. | Class | htsjdk.samtools | HtsJDK |
|
AlignmentSpan | A span of reads on a single reference. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
Allele | Immutable representation of an allele. | Class | htsjdk.variant.variantcontext | HtsJDK |
|
AsciiFeatureCodec | A convenience base class for codecs that want to read in features from ASCII lines. | Class | htsjdk.tribble | HtsJDK |
|
AsciiLineReader | A simple class that provides readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader. | Class | htsjdk.tribble.readers | HtsJDK |
|
AsciiLineReaderIterator | A class that iterates over the lines and line positions in an AsciiLineReader. | Class | htsjdk.tribble.readers | HtsJDK |
|
AsciiWriter | Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion. | Class | htsjdk.samtools.util | HtsJDK |
|
AsyncFastqWriter | | Class | htsjdk.samtools.fastq | HtsJDK |
|
AsynchronousLineReader | A LineReader implementation that delegates the work of reading and fetching lines to another thread. | Class | htsjdk.tribble.readers | HtsJDK |
|
AsyncVariantContextWriter | AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output. | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
BamFileIoUtils | | Class | htsjdk.samtools | HtsJDK |
|
BAMFileSpan | An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BAMIndex | A basic interface for querying BAM indices. | Interface | htsjdk.samtools | HtsJDK |
|
BAMIndexer | Class for both constructing BAM index content and writing it out. | Class | htsjdk.samtools | HtsJDK |
|
BAMIndexMetaData | Metadata about the bam index contained within the bam index. | Class | htsjdk.samtools | HtsJDK |
|
BamIndexValidator | Class to validate (at two different levels of thoroughness) the index for a BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BAMRecord | Wrapper class for binary BAM records. | Class | htsjdk.samtools | HtsJDK |
|
BAMRecordCodec | Class for translating between in-memory and disk representation of BAMRecord. | Class | htsjdk.samtools | HtsJDK |
|
BaseCategory | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
BaseCategoryType | enum BaseCategoryTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
BaseQualityScore | A read feature representing a single quality score in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
Bases | | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
BasicFastqWriter | In general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some cases in which that behavior is explicitly not wanted. | Class | htsjdk.samtools.fastq | HtsJDK |
|
BCF2Codec | | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCF2Decoder | | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCF2Encoder | See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
BCF2FieldEncoder | See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
BCF2FieldWriter | See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
BCF2FieldWriterManager | See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
BCF2GenotypeFieldDecoders | An efficient scheme for building and obtaining specialized genotype field decoders. | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCF2LazyGenotypesDecoder | Lazy version of genotypes decoder for BCF2 genotypesSince:5/12Author:Mark DePristo | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCF2Type | BCF2 types and associated informationSince:05/12Author:depristo | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCF2Utils | Common utilities for working with BCF2 files Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type) | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BCFVersion | | Class | htsjdk.variant.bcf2 | HtsJDK |
|
BEDCodec | Codec for parsing BED file, as described by UCSC See https://genome. | Class | htsjdk.tribble.bed | HtsJDK |
|
BEDFeature | | Interface | htsjdk.tribble.bed | HtsJDK |
|
BetaIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
Bin | An individual bin in a BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BinaryCodec | Encapsulates file representation of various primitive data types. | Class | htsjdk.samtools.util | HtsJDK |
|
BinaryFeatureCodec | | Class | htsjdk.tribble | HtsJDK |
|
BinaryTagCodec | Converter between disk and in-memory representation of a SAMRecord tag. | Class | htsjdk.samtools | HtsJDK |
|
BinList | Provides a list of all bins which could exist in the BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BinningIndexBuilder | Builder for a BinningIndexContent object. | Class | htsjdk.samtools | HtsJDK |
|
BinningIndexContent | In-memory representation of the binning index for a single reference. | Class | htsjdk.samtools | HtsJDK |
|
BitCodec | An interface that defines requirements for serializing/deserializing objects into and from a bit stream. | Interface | htsjdk.samtools.cram.encoding | HtsJDK |
|
BitInputStream | An interface to describe the requirements for reading bit data as opposed to bytes. | Interface | htsjdk.samtools.cram.io | HtsJDK |
|
BitOutputStream | An interface to describe the requirements for writing out bits as opposed to bytes. | Interface | htsjdk.samtools.cram.io | HtsJDK |
|
Block | Class representing CRAM block concept and some methods to operate with block content. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
Block | | Class | htsjdk.tribble.index | HtsJDK |
|
BlockCompressedFilePointerUtil | Static for manipulating virtual file pointers in BGZF files. | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedInputStream | | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedOutputStream | Writer for a file that is a series of gzip blocks (BGZF format). | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedStreamConstants | | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressionMethod | enum BlockCompressionMethodEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
BlockContentType | enum BlockContentTypeEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
BlockGunzipper | Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[]. | Class | htsjdk.samtools.util | HtsJDK |
|
BrowseableBAMIndex | An index interface with additional functionality for querying and inspecting the structure of a BAM index. | Interface | htsjdk.samtools | HtsJDK |
|
BufferedLineReader | than AsciiLineReaderImpl. | Class | htsjdk.samtools.util | HtsJDK |
|
ByteArrayLenEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ByteArraySeekableStream | Created by vadim on 23/03/2015. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
ByteArrayStopEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ChrIndex | | Interface | htsjdk.tribble.index | HtsJDK |
|
Chunk | A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. | Class | htsjdk.samtools | HtsJDK |
|
Cigar | A list of CigarElements, which describes how a read aligns with the reference. | Class | htsjdk.samtools | HtsJDK |
|
CigarElement | One component of a cigar string. | Class | htsjdk.samtools | HtsJDK |
|
CigarOperator | The operators that can appear in a cigar string, and information about their disk representations. | Class | htsjdk.samtools | HtsJDK |
|
CigarUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
CloseableIterator | This interface is used by iterators that use releasable resources during iteration. | Interface | htsjdk.samtools.util | HtsJDK |
|
CloseableTribbleIterator | The basic iterator we use in Tribble, which allows closing and basic iteration. | Interface | htsjdk.tribble | HtsJDK |
|
CloserUtil | Utility to close things that implement Closeable WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, and | Class | htsjdk.samtools.util | HtsJDK |
|
CodecLineParsingException | a generic exception we use if the codec has trouble parsing the line its givenAuthor:aaronSee Also:Serialized Form | Class | htsjdk.tribble.exception | HtsJDK |
|
CodeUtil | Miscellaneous util methods that don't fit anywhere else. | Class | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil | Small utility methods for dealing with collection classes. | Class | htsjdk.samtools.util | HtsJDK |
|
CommonInfo | Common utility routines for VariantContext and GenotypeAuthor:depristoSee Also:Serialized Form | Class | htsjdk.variant.variantcontext | HtsJDK |
|
ComparableTuple | A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements. | Class | htsjdk.samtools.util | HtsJDK |
|
CompoundFilter | A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false. | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
CompressionHeader | | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
CompressionHeaderFactory | A class responsible for decisions about which encodings to use for a given set of records. | Class | htsjdk.samtools.cram.build | HtsJDK |
|
Container | | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
ContainerFactory | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
ContainerIO | Methods to read and write CRAM containers. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
ContainerParser | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
ContentDigests | | Class | htsjdk.samtools.cram.digest | HtsJDK |
|
CoordinateSortedPairInfoMap | Holds info about a mate pair for use when processing a coordinate sorted file. | Class | htsjdk.samtools | HtsJDK |
|
CoordMath | | Class | htsjdk.samtools.util | HtsJDK |
|
CoordSpanInputSteam | An input stream that wraps a SeekableStream to produce only bytes specified within coordinates. | Class | htsjdk.samtools.util | HtsJDK |
|
CountingInputStream | An input stream that counts the bytes read from it. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
CountRecords | An example of how to index a feature file, and then count all the records in the file. | Class | htsjdk.tribble.example | HtsJDK |
|
CRAIEntry | A class representing CRAI index entry: file and alignment offsets for each slice. | Class | htsjdk.samtools.cram | HtsJDK |
|
CRAIIndex | A collection of static methods to read, write and convert CRAI index. | Class | htsjdk.samtools.cram | HtsJDK |
|
Cram2SamRecordFactory | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
CramArray | Methods to read and write CRAM array of integers data type. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
CramCompressionRecord | | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
CramContainerIterator | An iterator of CRAM containers read from an InputStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
|
CRAMContainerStreamWriter | Class for writing SAMRecords into a series of CRAM containers on an output stream. | Class | htsjdk.samtools | HtsJDK |
|
CRAMException | Created by edwardk on 8/13/15. | Class | htsjdk.samtools.cram | HtsJDK |
|
CRAMFileReader | BAMFileReader analogue for CRAM files. | Class | htsjdk.samtools | HtsJDK |
|
CRAMFileWriter | | Class | htsjdk.samtools | HtsJDK |
|
CramHeader | A starting object when dealing with CRAM files. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
CRAMIndexer | Class for both constructing BAM index content and writing it out. | Class | htsjdk.samtools | HtsJDK |
|
CramInt | Methods to read and write CRAM int values as given in the file format specification. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
CramIO | A collection of methods to open and close CRAM files. | Class | htsjdk.samtools.cram.build | HtsJDK |
|
CRAMIterator | | Class | htsjdk.samtools | HtsJDK |
|
CramNormalizer | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
CramRecordReader | | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
CramSpanContainerIterator | An iterator of CRAM containers read from locations in SeekableStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
|
CramVersionPolicies | The class provides version-dependant rules and policies for CRAM data. | Class | htsjdk.samtools.cram.common | HtsJDK |
|
CramVersions | | Class | htsjdk.samtools.cram.common | HtsJDK |
|
CRC32InputStream | An input stream that calculates CRC32 of all the bytes passed through it. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
CRC32OutputStream | An output stream that calculates CRC32 checksum of all the bytes written through the stream. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
CustomReaderFactory | Factory for creating custom readers for accessing API based resources, The configuration is controlled via custom_reader property (@see Defaults). | Class | htsjdk.samtools | HtsJDK |
|
DataReader | A basic interface for reading data. | Interface | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
DataReaderFactory | | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
DataSeries | An annotation to denote a data series field in a java class. | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
DataSeriesMap | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
DataSeriesType | Data series types known to CRAM. | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
DataWriter | A basic interface defining a writer. | Interface | htsjdk.samtools.cram.encoding.writer | HtsJDK |
|
DataWriterFactory | | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK |
|
DateParser | NOTE: This code has been taken from w3. | Class | htsjdk.samtools.util | HtsJDK |
|
DefaultBitInputStream | | Class | htsjdk.samtools.cram.io | HtsJDK |
|
DefaultBitOutputStream | | Class | htsjdk.samtools.cram.io | HtsJDK |
|
Defaults | Embodies defaults for global values that affect how the SAM JDK operates. | Class | htsjdk.samtools | HtsJDK |
|
DefaultSAMRecordFactory | Default factory for creating SAM and BAM records used by the SAMFileReader classes. | Class | htsjdk.samtools | HtsJDK |
|
DeflaterFactory | Create zlib-based Deflater if JNI library and other require libraries are available, otherwise create standard Java 7 has its own Deflater implementation (libzip. | Class | htsjdk.samtools.util.zip | HtsJDK |
|
DelegatingIterator | Simple iterator class that delegates all method calls to an underlying iterator. | Class | htsjdk.samtools.util | HtsJDK |
|
Deletion | A read feature representing a deletion of one or more bases similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
DiploidGenotype | enum DiploidGenotype Enum describing all possible combinations of diploid genotype variations; | Class | htsjdk.tribble.gelitext | HtsJDK |
|
DiskBackedQueue | A single-ended FIFO queue. | Class | htsjdk.samtools.util | HtsJDK |
|
DiskBasedBAMFileIndex | A class for reading BAM file indices, hitting the disk once per query. | Class | htsjdk.samtools | HtsJDK |
|
DownsamplingIterator | Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded. | Class | htsjdk.samtools | HtsJDK |
|
DownsamplingIteratorFactory | A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria. | Class | htsjdk.samtools | HtsJDK |
|
DuplicateReadFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
DuplicateScoringStrategy | This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates). | Class | htsjdk.samtools | HtsJDK |
|
DuplicateSet | Stores a set of records that are duplicates of each other. | Class | htsjdk.samtools | HtsJDK |
|
DuplicateSetIterator | An iterator of sets of duplicates. | Class | htsjdk.samtools | HtsJDK |
|
DynamicIndexCreator | A DynamicIndexCreator creates the proper index based on an IndexFactory. | Class | htsjdk.tribble.index | HtsJDK |
|
EnaRefService | | Class | htsjdk.samtools.cram.ref | HtsJDK |
|
Encoding | An interface to describe how a data series is encoded. | Interface | htsjdk.samtools.cram.encoding | HtsJDK |
|
EncodingFactory | A helper class to instantiate an appropriate Encoding for a given DataSeriesType and | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
EncodingID | Encoding ID as defined in the CRAM specs. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
EncodingKey | | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
EncodingParams | | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
ExampleBinaryCodec | An example binary codec that encodes / decodes contig / start / stop values via DataInputStreamsAuthor:Mark DePristo | Class | htsjdk.tribble.example | HtsJDK |
|
ExampleSamUsage | | Class | htsjdk.samtools.example | HtsJDK |
|
ExposedByteArrayOutputStream | | Class | htsjdk.samtools.cram.io | HtsJDK |
|
ExternalByteArrayEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ExternalByteEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ExternalCompression | Methods to provide CRAM external compression/decompression features. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
ExternalCompressor | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ExternalIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ExternalLongEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
FailsVendorReadQualityFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
FastaSequenceFile | | Class | htsjdk.samtools.reference | HtsJDK |
|
FastaSequenceIndex | Reads a fasta index file (. | Class | htsjdk.samtools.reference | HtsJDK |
|
FastGenotype | This class encompasses all the basic information about a genotype. | Class | htsjdk.variant.variantcontext | HtsJDK |
|
FastLineReader | Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance. | Class | htsjdk.samtools.util | HtsJDK |
|
FastqConstants | | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqQualityFormat | enum FastqQualityFormatEnumeration for FastQ quality score formats formats. | Class | htsjdk.samtools.util | HtsJDK |
|
FastqReader | Reads a FASTQ file with four lines per record. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqRecord | Represents a fastq record, fairly literally, i. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqWriter | Simple interface for a class that can write out fastq records. | Interface | htsjdk.samtools.fastq | HtsJDK |
|
FastqWriterFactory | Factory class for creating FastqWriter objects. | Class | htsjdk.samtools.fastq | HtsJDK |
|
Feature | Represents a locus on a reference sequence. | Interface | htsjdk.tribble | HtsJDK |
|
FeatureCodec | The base interface for classes that read in features. | Interface | htsjdk.tribble | HtsJDK |
|
FeatureCodecHeader | A class to represent a header of a feature containing file. | Class | htsjdk.tribble | HtsJDK |
|
FeatureReader | the basic interface that feature sources need to matchCloseableTribbleIter | Interface | htsjdk.tribble | HtsJDK |
|
FileAppendStreamLRUCache | LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams than resource limits will allow. | Class | htsjdk.samtools.util | HtsJDK |
|
FileTruncatedException | Thrown when it is possible to detect that a SAM or BAM file is truncated. | Class | htsjdk.samtools | HtsJDK |
|
FilteringIterator | Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter. | Class | htsjdk.samtools.filter | HtsJDK |
|
FilteringIterator | A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter. | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
FixBAMFile | | Class | htsjdk.samtools | HtsJDK |
|
FormatUtil | Simple class used to format object values into a standard format for printing. | Class | htsjdk.samtools.util | HtsJDK |
|
FTPClient | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPHelper | | Class | htsjdk.tribble.util | HtsJDK |
|
FTPReply | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPStream | A "non-seekable" ftp stream. | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPUtils | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FullBEDFeature | Object for full BED file. | Class | htsjdk.tribble.bed | HtsJDK |
|
GammaIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
GeliTextCodec | A codec for parsing geli text files, which is the text version of the geli binary format. | Class | htsjdk.tribble.gelitext | HtsJDK |
|
GeliTextFeature | Class GeliTextFeature This is a feature for the Geli text object, which is the text version of the Geli binary genotyping format. | Class | htsjdk.tribble.gelitext | HtsJDK |
|
GeneralUtils | | Class | htsjdk.variant.utils | HtsJDK |
|
GenomicIndexUtil | | Class | htsjdk.samtools | HtsJDK |
|
Genotype | This class encompasses all the basic information about a genotype. | Class | htsjdk.variant.variantcontext | HtsJDK |
|
GenotypeBuilder | A builder class for genotypes Provides convenience setter methods for all of the Genotype field | Class | htsjdk.variant.variantcontext | HtsJDK |
|
GenotypeLikelihoods | | Class | htsjdk.variant.variantcontext | HtsJDK |
|
GenotypeQualityFilter | A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants). | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
GenotypesContext | Represents an ordered collection of Genotype objectsSee Also:Serialized Form | Class | htsjdk.variant.variantcontext | HtsJDK |
|
GenotypeType | Summary types for Genotype objectsSince:Date createdAuthor:Your Name | Class | htsjdk.variant.variantcontext | HtsJDK |
|
GolombIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
GolombLongEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
GolombRiceIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
HardClip | A read feature representing a hard clip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
HardyWeinbergCalculation | This class calculates a HardyWeinberg p-value given three values representing the observed frequences of homozygous and heterozygous genotypes in the | Class | htsjdk.tribble.util.popgen | HtsJDK |
|
Header | A header for a metrics file. | Interface | htsjdk.samtools.metrics | HtsJDK |
|
HeterozygosityFilter | A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false). | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
Histogram | Class for computing and accessing histogram type data. | Class | htsjdk.samtools.util | HtsJDK |
|
HTTPHelper | Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes. | Class | htsjdk.tribble.util | HtsJDK |
|
HttpUtils | | Class | htsjdk.samtools.util | HtsJDK |
|
HuffmanByteEncoding | | Class | htsjdk.samtools.cram.encoding.huffman.codec | HtsJDK |
|
HuffmanCode | | Class | htsjdk.samtools.cram.encoding.huffman | HtsJDK |
|
HuffmanIntegerEncoding | | Class | htsjdk.samtools.cram.encoding.huffman.codec | HtsJDK |
|
HuffmanTree | | Class | htsjdk.samtools.cram.encoding.huffman | HtsJDK |
|
Index | Interface for all index implementations. | Class | htsjdk.tribble.index | HtsJDK |
|
IndexCreator | | Interface | htsjdk.tribble.index | HtsJDK |
|
IndexedFastaSequenceFile | A fasta file driven by an index for fast, concurrent lookups. | Class | htsjdk.samtools.reference | HtsJDK |
|
IndexFactory | Factory class for creating indexes. | Class | htsjdk.tribble.index | HtsJDK |
|
IndexToTable | | Class | htsjdk.tribble.example | HtsJDK |
|
IndicesAreEqual | | Class | htsjdk.tribble.example | HtsJDK |
|
InputStreamUtils | Convenience methods to read from InputStream. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
InsertBase | A read feature representing a single insert base. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
Insertion | A read feature representing a multi-base insertion. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
InsertSizeFilter | Filter things that fall outside a specified range of insert sizes. | Class | htsjdk.samtools.filter | HtsJDK |
|
IntelDeflater | This is a copy of java. | Class | htsjdk.samtools.util.zip | HtsJDK |
|
Interval | Represents a simple interval on a sequence. | Class | htsjdk.samtools.util | HtsJDK |
|
Interval | Quick and dirty interval class Describes a genomic interval and where in a file information for that | Class | htsjdk.tribble.index.interval | HtsJDK |
|
IntervalFilter | Filter SAMRecords so that only those that overlap the given list of intervals. | Class | htsjdk.samtools.filter | HtsJDK |
|
IntervalIndexCreator | | Class | htsjdk.tribble.index.interval | HtsJDK |
|
IntervalList | Represents a list of intervals against a reference sequence that can be written to and read from a file. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalListReferenceSequenceMask | Serve up loci of interest based on an interval list. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTree | A Red-Black tree with intervals for keys. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTree | An implementation of an interval tree, following the explanation. | Class | htsjdk.tribble.index.interval | HtsJDK |
|
IntervalTreeIndex | Index based on an interval treeAuthor:jrobinsoSee Also:IntervalTree | Class | htsjdk.tribble.index.interval | HtsJDK |
|
IntervalTreeMap | Utility class that implements an interval map. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
IntGenotypeFieldAccessors | A convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values. | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
IntHashMap | A hash map that uses primitive ints for the key rather than objects. | Class | htsjdk.samtools.cram.common | HtsJDK |
|
IOUtil | Miscellaneous stateless static IO-oriented methods. | Class | htsjdk.samtools.util | HtsJDK |
|
ISeekableStreamFactory | Factory for creating SeekableStreams based on URLs/paths. | Interface | htsjdk.samtools.seekablestream | HtsJDK |
|
Iso8601Date | Use this type rather than java. | Class | htsjdk.samtools.util | HtsJDK |
|
IterableAdapter | Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop. | Class | htsjdk.samtools.util | HtsJDK |
|
IterableOnceIterator | Abstract implementation of an iterator that also implements Iterable (to return itself) so that it can be used if for() loops. | Class | htsjdk.samtools.util | HtsJDK |
|
Iterables | | Class | htsjdk.samtools.util | HtsJDK |
|
ITF8 | Methods to read and write int values as per ITF8 specification in CRAM. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
JavascriptSamRecordFilter | javascript based read filter The script puts the following variables in the script context: | Class | htsjdk.samtools.filter | HtsJDK |
|
JavascriptVariantFilter | javascript based variant filter The script puts the following variables in the script context: | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
Lazy | Simple utility for building an on-demand (lazy) object-initializer. | Class | htsjdk.samtools.util | HtsJDK |
|
LazyGenotypesContext | Lazy-loading GenotypesContext. | Class | htsjdk.variant.variantcontext | HtsJDK |
|
LiftOver | Java port of UCSC liftOver. | Class | htsjdk.samtools.liftover | HtsJDK |
|
LinearIndex | The linear index associated with a given reference in a BAM index. | Class | htsjdk.samtools | HtsJDK |
|
LinearIndex | Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates). | Class | htsjdk.tribble.index.linear | HtsJDK |
|
LinearIndexCreator | For creating a LinearIndex from a stream of features. | Class | htsjdk.tribble.index.linear | HtsJDK |
|
LineIterator | A very simple descriptor for line-iterables. | Interface | htsjdk.tribble.readers | HtsJDK |
|
LineIteratorImpl | A simple iterator over the elements in LineReader. | Class | htsjdk.tribble.readers | HtsJDK |
|
LineReader | Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else. | Interface | htsjdk.samtools.util | HtsJDK |
|
LineReader | Interface for line-oriented readers. | Interface | htsjdk.tribble.readers | HtsJDK |
|
LineReaderUtil | A collection of factories for generating LineReaders. | Class | htsjdk.tribble.readers | HtsJDK |
|
ListMap | A Map class that holds a list of entries under each key instead of a single entry, and provides utility methods for adding an entry under a key. | Class | htsjdk.samtools.util | HtsJDK |
|
LittleEndianInputStream | Input stream with methods to convert byte arrays to numeric values using "little endian" order. | Class | htsjdk.tribble.util | HtsJDK |
|
LittleEndianOutputStream | | Class | htsjdk.tribble.util | HtsJDK |
|
Locatable | Any class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both ends | Interface | htsjdk.samtools.util | HtsJDK |
|
LocationAware | Describes API for getting current position in a stream, writer, or underlying file. | Interface | htsjdk.samtools.util | HtsJDK |
|
Locus | Location info about a locus. | Interface | htsjdk.samtools.util | HtsJDK |
|
LocusComparator | compares first by sequence index then by positionAuthor:Doug Voet (dvoet at broadinstitute dot org)See Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
LocusImpl | Simple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations. | Class | htsjdk.samtools.util | HtsJDK |
|
Log | A wafer thin wrapper around System. | Class | htsjdk.samtools.util | HtsJDK |
|
LongLineBufferedReader | A variant of BufferedReader with improved performance reading files with long lines. | Class | htsjdk.tribble.readers | HtsJDK |
|
LTF8 | Methods to read and write LTF8 as per CRAM specs. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
MappingQualityFilter | Filter things with low mapping quality. | Class | htsjdk.samtools.filter | HtsJDK |
|
MathUtils | | Class | htsjdk.tribble.util | HtsJDK |
|
Md5CalculatingInputStream | Class to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue. | Class | htsjdk.samtools.util | HtsJDK |
|
Md5CalculatingOutputStream | Class to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue. | Class | htsjdk.samtools.util | HtsJDK |
|
MergingIterator | An iterator over Iterators that return Ts. | Class | htsjdk.samtools.util | HtsJDK |
|
MergingSamRecordIterator | Provides an iterator interface for merging multiple underlying iterators into a single iterable stream. | Class | htsjdk.samtools | HtsJDK |
|
MetricBase | A base class from which all Metric classes should inherit. | Class | htsjdk.samtools.metrics | HtsJDK |
|
MetricsFile | Contains a set of metrics that can be written to a file and parsed back again. | Class | htsjdk.samtools.metrics | HtsJDK |
|
Murmur3 | Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling. | Class | htsjdk.samtools.util | HtsJDK |
|
MutableIndex | Some Index implementations can be modified in memory. | Interface | htsjdk.tribble.index | HtsJDK |
|
MutableInt | | Class | htsjdk.samtools.cram.common | HtsJDK |
|
NameAwareCodec | Created by IntelliJ IDEA. | Interface | htsjdk.tribble | HtsJDK |
|
NotPrimaryAlignmentFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
NotPrimarySkippingIterator | Wrapper around SAMRecord iterator that skips over non-primary elements. | Class | htsjdk.samtools | HtsJDK |
|
NullEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
Objects | Subset of JDK7's Objects for non-JDK7 support. | Class | htsjdk.samtools.util | HtsJDK |
|
Options | Available writer options for VariantContextWritersSince:5/12Author:Mark DePristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
|
OverclippedReadFilter | Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e. | Class | htsjdk.samtools.filter | HtsJDK |
|
OverlapDetector | Utility class to efficiently do in memory overlap detection between a large set of mapping like objects, and one or more candidate mappings. | Class | htsjdk.samtools.util | HtsJDK |
|
Padding | A read feature representing padding, similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
ParsingUtils | | Class | htsjdk.tribble.util | HtsJDK |
|
PassingVariantFilter | A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants). | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
|
PeekableIterator | | Class | htsjdk.samtools.util | HtsJDK |
|
PeekIterator | Wrapper around an iterator that enables non-destructive peeking at the next element that would be returned by next() | Class | htsjdk.samtools.util | HtsJDK |
|
Positional | Minimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other reader-like features. | Interface | htsjdk.tribble.readers | HtsJDK |
|
PositionalBufferedStream | A wrapper around an InputStream which performs it's own buffering, and keeps track of the position. | Class | htsjdk.tribble.readers | HtsJDK |
|
PreservationPolicy | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
ProcessExecutor | Utility class that will execute sub processes via Runtime. | Class | htsjdk.samtools.util | HtsJDK |
|
ProfileIndexReading | | Class | htsjdk.tribble.example | HtsJDK |
|
ProgressLogger | Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records. | Class | htsjdk.samtools.util | HtsJDK |
|
ProgressLoggerInterface | An interface defining the record() methods of the Picard-public ProgressLogger implementation. | Interface | htsjdk.samtools.util | HtsJDK |
|
QualityEncodingDetector | Utility for determining the type of quality encoding/format (see FastqQualityFormat) used in a SAM/BAM or Fastq. | Class | htsjdk.samtools.util | HtsJDK |
|
QualityScorePreservation | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
QualityScoreTreatment | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
QualityScoreTreatmentType | enum QualityScoreTreatmentTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
QualityUtil | Utility class for working with quality scores and error probabilities. | Class | htsjdk.samtools.util | HtsJDK |
|
QueryInterval | Interval relative to a reference, for querying a BAM file. | Class | htsjdk.samtools | HtsJDK |
|
RANS | | Class | htsjdk.samtools.cram.encoding.rans | HtsJDK |
|
ReadBase | A read feature representing a single base with associated quality score. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
ReadCategory | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
ReadCategoryType | enum ReadCategoryTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
ReadFeature | An interface to capture data in read coordinates. | Interface | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
ReadNameFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
ReadTag | CRAM counterpart of SAMTag. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
ReferenceCache | That is a thread-safe wrapper for a list of cache Reference objects. | Class | htsjdk.samtools.sra | HtsJDK |
|
ReferenceSequence | Wrapper around a reference sequence that has been read from a reference file. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFile | An interface for working with files of reference sequences regardless of the file formatRetrieves the complete sequence described by this contig. | Interface | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFileFactory | Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFileWalker | Manages a ReferenceSequenceFile. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceMask | Interface for specifying loci of interest for genotype calling and other operations. | Interface | htsjdk.samtools.util | HtsJDK |
|
ReferenceSource | | Class | htsjdk.samtools.cram.ref | HtsJDK |
|
ReferenceTracks | | Class | htsjdk.samtools.cram.ref | HtsJDK |
|
RefSeqIdReader | A reader that only keeps track of alignment spans. | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
RefSkip | A read feature representing a reference skip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
RelativeIso8601Date | Like Iso8601Date, but also comes in a "lazy now" flavor. | Class | htsjdk.samtools.util | HtsJDK |
|
RemoteURLHelper | Determines appropriate helper based on protocol (ftp/http), and then delegates. | Class | htsjdk.tribble.util | HtsJDK |
|
ReservedTagConstants | | Class | htsjdk.samtools | HtsJDK |
|
ResourceLimitedMap | LRU collection class for managing objects that place some resource burden such that not too many of them can existing in the VM at one time, but they can be reconstructed ias necessary. | Class | htsjdk.samtools.util | HtsJDK |
|
ResourceLimitedMapFunctor | c. | Interface | htsjdk.samtools.util | HtsJDK |
|
RuntimeEOFException | Thrown by various codecs to indicate EOF without having to clutter the API with throws clausesSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
RuntimeIOException | Thrown by various IO classes to indicate IOException without having to clutter the API with throws clausesSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
RuntimeScriptException | Thrown by classes handling script engines like the javascript-based filters for SAM/VCFSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
Sam2CramRecordFactory | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
SAMBinaryTagAndUnsignedArrayValue | Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value. | Class | htsjdk.samtools | HtsJDK |
|
SAMBinaryTagAndValue | Holds a SAMRecord attribute and the tagname (in binary form) for that attribute. | Class | htsjdk.samtools | HtsJDK |
|
SAMException | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileHeader | Header information from a SAM or BAM file. | Class | htsjdk.samtools | HtsJDK |
|
SamFileHeaderMerger | Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups | Class | htsjdk.samtools | HtsJDK |
|
SAMFileReader | Class for reading and querying SAM/BAM files. | Class | htsjdk.samtools | HtsJDK |
|
SamFiles | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileSource | Represents the origin of a SAM record. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileSpan | A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query. | Interface | htsjdk.samtools | HtsJDK |
|
SAMFileTruncatedReader | A truncated form of a SAMFileReader that iterates over a limited number of records. | Class | htsjdk.samtools | HtsJDK |
|
SamFileValidator | Validates SAM files as follows: checks sam file header for sequence dictionarychecks sam file header for read groupsfor each sam record | Class | htsjdk.samtools | HtsJDK |
|
SAMFileWriter | Interface for SAMText and BAM file writers. | Interface | htsjdk.samtools | HtsJDK |
|
SAMFileWriterFactory | Create a writer for writing SAM, BAM, or CRAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileWriterImpl | Base class for implementing SAM writer with any underlying format. | Class | htsjdk.samtools | HtsJDK |
|
SAMFlag | SAM flags as enum, to be used in GUI, menu, etc. | Class | htsjdk.samtools | HtsJDK |
|
SAMFormatException | Thrown when a SAM file being read or decoded (text or binary) looks bad. | Class | htsjdk.samtools | HtsJDK |
|
SAMHeaderRecordComparator | Provides ordering based on SAM header records' attribute values. | Class | htsjdk.samtools | HtsJDK |
|
SamIndexes | A helper class to read BAI and CRAI indexes. | Class | htsjdk.samtools | HtsJDK |
|
SamInputResource | Describes a SAM-like resource, including its data (where the records are), and optionally an index. | Class | htsjdk.samtools | HtsJDK |
|
SAMLineParser | this class enables creation of a SAMRecord object from a String in SAM text format. | Class | htsjdk.samtools | HtsJDK |
|
SamLocusIterator | Iterator that traverses a SAM File, accumulating information on a per-locus basis. | Class | htsjdk.samtools.util | HtsJDK |
|
SamPairUtil | | Class | htsjdk.samtools | HtsJDK |
|
SAMProgramRecord | In-memory representation of @PG SAM header record. | Class | htsjdk.samtools | HtsJDK |
|
SamReader | Describes functionality for objects that produce SAMRecords and associated information. | Interface | htsjdk.samtools | HtsJDK |
|
SamReaderFactory | Describes the functionality for producing SamReader, and offers a handful of static generators. | Class | htsjdk.samtools | HtsJDK |
|
SAMReadGroupRecord | Header information about a read group. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecord | Java binding for a SAM file record. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordComparator | Interface for comparators that define the various SAM sort orders. | Interface | htsjdk.samtools | HtsJDK |
|
SAMRecordCoordinateComparator | Comparator for sorting SAMRecords by coordinate. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordDuplicateComparator | Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates). | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordFactory | Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files. | Interface | htsjdk.samtools | HtsJDK |
|
SamRecordFilter | API for filtering SAMRecordsDetermines whether a SAMRecord matches this filter | Interface | htsjdk.samtools.filter | HtsJDK |
|
SamRecordIntervalIteratorFactory | Create an iterator over a SAMFileReader that only returns reads that overlap one of the intervals in an interval list. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMRecordIterator | A general interface that adds functionality to a CloseableIterator of SAMRecords. | Interface | htsjdk.samtools | HtsJDK |
|
SAMRecordQueryHashComparator | SAMRecord comparator that provides an ordering based on a hash of the queryname. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordQueryNameComparator | Comparator for "queryname" ordering of SAMRecords. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordSetBuilder | Factory class for creating SAMRecords for testing purposes. | Class | htsjdk.samtools | HtsJDK |
|
SamRecordTrackingBuffer | This class stores SAMRecords for return. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMRecordUtil | | Class | htsjdk.samtools | HtsJDK |
|
SamRecordWithOrdinal | A little class to store the unique index associated with this record. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMSequenceDictionary | Collection of SAMSequenceRecords. | Class | htsjdk.samtools | HtsJDK |
|
SAMSequenceDictionaryExtractor | Tiny class for automatically loading a SAMSequenceDictionary given a fileAuthor:farjoun on 2/25/2014 | Class | htsjdk.variant.utils | HtsJDK |
|
SAMSequenceRecord | Header information about a reference sequence. | Class | htsjdk.samtools | HtsJDK |
|
SAMSortOrderChecker | Encapsulates simple check for SAMRecord order. | Class | htsjdk.samtools | HtsJDK |
|
SamStreams | | Class | htsjdk.samtools | HtsJDK |
|
SAMTag | The standard tags for a SAM record that are defined in the SAM spec. | Class | htsjdk.samtools | HtsJDK |
|
SAMTagUtil | Facility for converting between String and short representation of a SAM tag. | Class | htsjdk.samtools | HtsJDK |
|
SAMTestUtil | Misc methods for SAM-related unit tests. | Class | htsjdk.samtools | HtsJDK |
|
SAMTextHeaderCodec | Parser for a SAM text header, and a generator of SAM text header. | Class | htsjdk.samtools | HtsJDK |
|
SAMTextWriter | Writer for text-format SAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMTools | Command line utility for manipulating SAM/BAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMUtils | | Class | htsjdk.samtools | HtsJDK |
|
SAMValidationError | Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type. | Class | htsjdk.samtools | HtsJDK |
|
Scores | A read feature representing a contiguous stretch of quality scores in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
SecondaryAlignmentFilter | SamRecordFilter that filters out secondary alignments, but not supplemental alignments. | Class | htsjdk.samtools.filter | HtsJDK |
|
SecondaryOrSupplementaryFilter | Filter out SAMRecords with NotPrimaryAlignment or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator, | Class | htsjdk.samtools.filter | HtsJDK |
|
SecondaryOrSupplementarySkippingIterator | Wrapper around SAMRecord iterator that skips over secondary and supplementary elements. | Class | htsjdk.samtools | HtsJDK |
|
SeekableBufferedStream | A wrapper class to provide buffered read access to a SeekableStream. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFileStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFTPStream | Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFTPStreamHelper | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableHTTPStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableMemoryStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableStreamFactory | Singleton class for getting SeekableStreams from URL/paths Applications using this library can set their own factory | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SequenceUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
SimpleBEDFeature | Feature from a BED file without exon blocks. | Class | htsjdk.tribble.bed | HtsJDK |
|
SimpleFeature | A simple concrete Feature. | Class | htsjdk.tribble | HtsJDK |
|
Slice | CRAM slice is a logical union of blocks into for example alignment slices. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
SnappyLoader | If Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream. | Class | htsjdk.samtools.util | HtsJDK |
|
SnpFilter | A Predicate on VariantContexts that returns true at sites that are SNPsAuthor:Yossi Farjoun | Class | htsjdk.variant.variantcontext.filter | HtsJDK |
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SoftClip | A read feature representing a soft clip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
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SolexaNoiseFilter | Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact. | Class | htsjdk.samtools.filter | HtsJDK |
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SolexaQualityConverter | Optimized method for converting Solexa ASCII qualities into Phred scores. | Class | htsjdk.samtools.util | HtsJDK |
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SortingCollection | Collection to which many records can be added. | Class | htsjdk.samtools.util | HtsJDK |
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SortingLongCollection | Accumulate a list of longs that can then be sorted in natural order and iterated over. | Class | htsjdk.samtools.util | HtsJDK |
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SortingVariantContextWriter | | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
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SQTagUtil | Utility methods for encoding and decoding the SQ tag value of SAMRecord. | Class | htsjdk.samtools | HtsJDK |
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SRAAccession | Describes a single SRA accession for SRA read collection Also provides app string functionality and allows to check if working SRA is supported on the running platform | Class | htsjdk.samtools.sra | HtsJDK |
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SRAAlignmentIterator | Iterator for aligned reads. | Class | htsjdk.samtools.sra | HtsJDK |
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SRAFileReader | | Class | htsjdk.samtools | HtsJDK |
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SRAIndex | Emulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works: | Class | htsjdk.samtools | HtsJDK |
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SRAIndexedSequenceFile | | Class | htsjdk.samtools.sra | HtsJDK |
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SRAIterator | | Class | htsjdk.samtools | HtsJDK |
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SRALazyRecord | Since SRA is a column oriented database, it is very inefficient to load all the fields at once. | Class | htsjdk.samtools.sra | HtsJDK |
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SRAUnalignmentIterator | Iterator for unaligned reads. | Class | htsjdk.samtools.sra | HtsJDK |
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SRAUtils | Provides some functionality which can be used by other classes Created by andrii. | Class | htsjdk.samtools.sra | HtsJDK |
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StopWatch | Utility to help in performance testing. | Class | htsjdk.samtools.util | HtsJDK |
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Strand | Enum for strand, which can be encoded as stringEnum Constant Summary | Class | htsjdk.tribble.annotation | HtsJDK |
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StringHeader | A simple header who's data type is a single String. | Class | htsjdk.samtools.metrics | HtsJDK |
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StringLineReader | is necessary because the String is in unicode. | Class | htsjdk.samtools.util | HtsJDK |
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StringUtil | Grab-bag of stateless String-oriented utilities. | Class | htsjdk.samtools.util | HtsJDK |
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SubexponentialIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
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Substitution | A substitution event captured in read coordinates. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
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SubstitutionMatrix | | Class | htsjdk.samtools.cram.structure | HtsJDK |
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TabixFeatureReader | | Class | htsjdk.tribble | HtsJDK |
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TabixFormat | The values in a Tabix header that define the format of the file being indexed, e. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIndex | This class represent a Tabix index that has been built in memory or read from a file. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIndexCreator | IndexCreator for Tabix. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIteratorLineReader | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixReader | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixUtils | | Class | htsjdk.tribble.util | HtsJDK |
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TagFilter | | Class | htsjdk.samtools.filter | HtsJDK |
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TagValueAndUnsignedArrayFlag | CVO to use as a method return value. | Class | htsjdk.samtools | HtsJDK |
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TempStreamFactory | Factory class for wrapping input and output streams for temporary files. | Class | htsjdk.samtools.util | HtsJDK |
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TestUtil | | Class | htsjdk.samtools.util | HtsJDK |
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TextCigarCodec | Convert between String and Cigar class representations of CIGAR. | Class | htsjdk.samtools | HtsJDK |
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TextTagCodec | Converter between SAM text representation of a tag, and in-memory Object representation. | Class | htsjdk.samtools | HtsJDK |
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TimeChannel | | Class | htsjdk.samtools.apps | HtsJDK |
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TimeRandomAccessFile | | Class | htsjdk.samtools.apps | HtsJDK |
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Tribble | | Class | htsjdk.tribble | HtsJDK |
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TribbleException | | Class | htsjdk.tribble | HtsJDK |
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TribbleIndexCreator | Base class for Tribble-specific index creators. | Class | htsjdk.tribble.index | HtsJDK |
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TribbleIndexedFeatureReader | A reader for text feature files (i. | Class | htsjdk.tribble | HtsJDK |
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TrimmingUtil | Utility code for performing quality trimming. | Class | htsjdk.samtools.util | HtsJDK |
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Tuple | A simple tuple class. | Class | htsjdk.samtools.util | HtsJDK |
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UnsortedFileException | an exception for when we've discovered that an input file is unsorted; sorted files are required by TribbleSee Also:Serialized Form | Class | htsjdk.tribble.exception | HtsJDK |
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URLHelper | Interface defining a helper class for dealing with URL resources. | Interface | htsjdk.tribble.util | HtsJDK |
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UserPasswordInput | | Interface | htsjdk.samtools.seekablestream | HtsJDK |
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ValidationStringency | enum ValidationStringencyHow strict to be when reading a SAM or BAM, beyond bare minimum validation. | Class | htsjdk.samtools | HtsJDK |
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VariantContext | High-level overview The VariantContext object is a single general class system for representing genetic variation data composed of: | Class | htsjdk.variant.variantcontext | HtsJDK |
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VariantContextBuilder | Builder class for VariantContext. | Class | htsjdk.variant.variantcontext | HtsJDK |
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VariantContextComparator | A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List provided at construction time, then by start position with each contig/chromosome. | Class | htsjdk.variant.variantcontext | HtsJDK |
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VariantContextFilter | API for filtering VariantContextsAuthor:Yossi Farjoun | Interface | htsjdk.variant.variantcontext.filter | HtsJDK |
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VariantContextUtils | | Class | htsjdk.variant.variantcontext | HtsJDK |
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VariantContextWriter | this class writes VCF filesattempt to close the VCF file | Interface | htsjdk.variant.variantcontext.writer | HtsJDK |
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VariantContextWriterBuilder | Provides methods for creating VariantContextWriters using the Builder pattern. | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
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VariantContextWriterFactory | Factory methods to create VariantContext writersSince:5/12Author:depristo | Class | htsjdk.variant.variantcontext.writer | HtsJDK |
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VCF3Codec | A feature codec for the VCF3 specification, to read older VCF files. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFCodec | A feature codec for the VCF 4 specification VCF is a text file format (most likely stored in a compressed manner). | Class | htsjdk.variant.vcf | HtsJDK |
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VCFCompoundHeaderLine | a base class for compound header lines, which include info lines and format lines (so far)See Also:Serialized Form | Class | htsjdk.variant.vcf | HtsJDK |
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VCFConstants | | Class | htsjdk.variant.vcf | HtsJDK |
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VCFContigHeaderLine | A special class representing a contig VCF header line. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFEncoder | Functions specific to encoding VCF records. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFFileReader | Simplified interface for reading from VCF/BCF files. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFFilterHeaderLine | | Class | htsjdk.variant.vcf | HtsJDK |
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VCFFormatHeaderLine | Class VCFFormatHeaderLine A class representing a key=value entry for genotype FORMAT fields in the VCF headerSee Also:Serialized Form | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeader | A class to represent a VCF header NOTE: This class stores header lines in lots of places. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeaderLine | Class VCFHeaderLine A class representing a key=value entry in the VCF header | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeaderLineCount | enum VCFHeaderLineCountthe count encodings we use for fields in VCF header lines | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeaderLineTranslator | | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeaderLineType | enum VCFHeaderLineTypethe type encodings we use for fields in VCF header lines | Class | htsjdk.variant.vcf | HtsJDK |
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VCFHeaderVersion | enum VCFHeaderVersioninformation that identifies each header version | Class | htsjdk.variant.vcf | HtsJDK |
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VCFIDHeaderLine | | Interface | htsjdk.variant.vcf | HtsJDK |
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VCFInfoHeaderLine | Class VCFInfoHeaderLine A class representing a key=value entry for INFO fields in the VCF header | Class | htsjdk.variant.vcf | HtsJDK |
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VCFRecordCodec | Writes VariantContext instances to an OutputStream without headers or metadata. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFSimpleHeaderLine | | Class | htsjdk.variant.vcf | HtsJDK |
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VCFStandardHeaderLines | Manages header lines for standard VCF INFO and FORMAT fields. | Class | htsjdk.variant.vcf | HtsJDK |
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VCFUtils | | Class | htsjdk.variant.vcf | HtsJDK |
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Version | A class to represent a version information, 3 number: major, minor and build number. | Class | htsjdk.samtools.cram.common | HtsJDK |
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VersionHeader | Header that stores information about the version of some piece of software or data used to create the metrics file. | Class | htsjdk.samtools.metrics | HtsJDK |
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WholeGenomeReferenceSequenceMask | | Class | htsjdk.samtools.util | HtsJDK |
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WholeReadClippedFilter | Filter SAMRecords so that only those that have at least one un-clipped base areAuthor:ktibbett@broadinstitute. | Class | htsjdk.samtools.filter | HtsJDK |
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Writer | | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK |